Recent content by Benjamin Buchfink

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    v2.0.1 released

    Added feature for using the tool in a distributed computing environment. (See here for details: http://www.diamondsearch.org/index.php?pages/distributed_computing/) Fixed an issue that could cause increased memory usage and runtimes in certain cases. Fixed a bug that could cause a crash when...
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    v2.0.0 released

    Added the sensitivity modes --very-sensitive and --ultra-sensitive. Both modes are designed for finding distant hits of <40% identity with a sensitivity similar to BLAST, with the ultra-sensitive mode being the slightly more sensitive mode. The --block-size/-b parameter is set to 0.4 and the...
  3. B

    v0.9.36 released

    Fixed a bug that could cause makedb to produce invalid database files when using taxonomy features. Fixed a bug that could cause a crash when running in query-indexed mode.
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    Hectic operation under WinServer 2019 / NVRAM / AMD Epyc config

    Hi Blaize, no idea about this error unfortunately. Could you maybe run diamond using the --log option and show me the output, that might help me narrow down things a bit.
  5. B

    Database was built with a newer version of Diamond and is incompatible.

    The issue has now also been fixed in the latest release.
  6. B

    Database was built with a newer version of Diamond and is incompatible.

    There was another bug, please try again using this commit: https://github.com/bbuchfink/diamond/commit/3f4da374b64be83584cd0c2cada42f2250bf924e (you have to check out the dev branch) You will also need to build the db file again.
  7. B

    Database was built with a newer version of Diamond and is incompatible.

    I found a potential issue. Please try again by compiling the latest commit from the github repository.
  8. B

    Database was built with a newer version of Diamond and is incompatible.

    There seems to be something going seriously wrong. If you got diamond from conda, could you instead try to download the binary from here and/or compile from source: https://github.com/bbuchfink/diamond/releases/tag/v0.9.35
  9. B

    Database was built with a newer version of Diamond and is incompatible.

    Please double check that you are using the same version for each call to diamond using diamond version. Also use diamond dbinfo -d <db_file> to check the database format version, it should be 3 for the latest version.
  10. B

    query fasta format issues

    Try to use the options --more-sensitive --masking 0 --comp-based-stats 0 -e 100. Still, Diamond is not ideal for mapping such short sequences.
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    v0.9.35 released

    Fixed a bug in diamond view that would cause high memory usage and erroneous output. Reduced the use of temporary disk space. Fixed a database compatibility issue with big endian architectures. Fixed a bug that would cause a crash for query sequences shorter than 5 letters in blastx mode. Fixed...
  12. B

    Error: Invalid taxonomic rank

    Support for the new ranks has been added in the latest release.
  13. B

    Would it be efficient if the blastp option used the same reference over multiple inputs?

    Yes that would certainly be viable. The block size does not affect the accuracy, higher numbers will only increase speed, but also memory usage.
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    Would it be efficient if the blastp option used the same reference over multiple inputs?

    If you can combine your databases to a larger one, that would be better. Diamond is more efficient the larger the query and database files. That is within certain limits, if your files are a couple of GB in size you can also run it separately.
  15. B

    Error: Invalid taxonomic rank

    It looks like NCBI has recently added a new rank (strain). I will provide an update to Diamond in the next days.
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